DReichLab / DReichLab/AdmixTools
f2 from qpgraph with NULL as outgroup
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- Dominant language
- C
- Stars
- 235
- Forks
- 76
- PR merge metrics
- No merged PRs in 30d
Description
Hi All,
I'm wondering what is the scale of f2 in qpgraph output? I set outgroup as NULL to turn off normalization but the resulting f2 seems to be normalized by heterozygosity somewhere. I tried to compute f2 and Fst myself, and my Fst agrees with qpgraph but f2 doens't.
I'm very grateful for the help.
Chi-Chun
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
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Research direction
Begin with the qpgraph output path and the handling of a NULL outgroup; the issue does not name a source file, test, or entry point. Reproduce the reported f2 and Fst comparison, then document whether disabling normalization changes f2 as expected and add a focused regression test if the behavior is confirmed.
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Assessment
- Tech stack
- c
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100